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Record Information
Version3.6
Creation Date2006-05-22 14:17:50 UTC
Update Date2016-02-11 01:05:36 UTC
HMDB IDHMDB02369
Secondary Accession NumbersNone
Metabolite Identification
Common Name9-cis-Retinoic acid
Description9-cis-retinoic acid is an active retinoid that regulates expression of retinoid responsive genes, serving as ligand for two classes of ligand-dependent transcription factors, the retinoic acid receptors and retinoid X receptors. Retinoids (vitamin A and its analogs) are essential dietary substances that are needed by mammals for reproduction, normal embryogenesis, growth, vision, and maintaining normal cellular differentiation and the integrity of the immune system. Within cells, retinoids regulate gene transcription acting through ligand-dependent transcription factors, the retinoic acid receptors (RARs), and the retinoid X receptors (RXRs). All-trans-retinoic acid binds only to RARs with high affinity, whereas its 9-cis isomer binds with high affinity to both RARs and RXRs. The actions of all-trans- and 9-cis-retinoic acid in regulating cellular responses are distinct and not interchangeable. (PMID: 9115228 ).
Structure
Thumb
Synonyms
ValueSource
(2E,4E,6Z,8E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acidChEBI
(7E,9Z,11E,13E)-Retinoic acidChEBI
9(Z)-Retinoic acidChEBI
9-cis-TretinoinChEBI
AlitretinoinaChEBI
AlitretinoineChEBI
AlitretinoinumChEBI
PanretinChEBI
PanretynChEBI
(2E,4E,6Z,8E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoateGenerator
(7E,9Z,11E,13E)-RetinoateGenerator
9(Z)-RetinoateGenerator
15-apo-beta-Caroten-15-OateHMDB
15-apo-beta-Caroten-15-Oic acidHMDB
9-cis-RetinoateHMDB
9-RetinoateHMDB
9-Retinoic acidHMDB
AberelHMDB
AberelaHMDB
AirolHMDB
AknotenHMDB
all-trans- Vitamin a1 acidHMDB
all-trans-b-RetinoateHMDB
all-trans-b-Retinoic acidHMDB
all-trans-beta-RetinoateHMDB
all-trans-beta-Retinoic acidHMDB
all-trans-Vitamin a acidHMDB
alpha-VitaminsyreHMDB
AtragenHMDB
AvitaHMDB
AvitoinHMDB
b-RetinoateHMDB
b-Retinoic acidHMDB
beta-RetinoateHMDB
beta-Retinoic acidHMDB
DermairolHMDB
EffedermHMDB
Epi-aberelHMDB
EudynaHMDB
Isotretinoin retinoateHMDB
Isotretinoin retinoic acidHMDB
Panretin gelHMDB
PanrexinHMDB
RenovaHMDB
RetacnylHMDB
Retin aHMDB
Retin-aHMDB
Retin-a microHMDB
RetinoateHMDB
Retinoic acidHMDB
RetinovaHMDB
trans-RetinoateHMDB
trans-Retinoic acidHMDB
trans-Vitamin a acidHMDB
TretinoinHMDB
Tretinoin/all-trans retinoateHMDB
Tretinoin/all-trans retinoic acidHMDB
TretinonHMDB
VesanoidHMDB
VesnaroidHMDB
Chemical FormulaC20H28O2
Average Molecular Weight300.4351
Monoisotopic Molecular Weight300.20893014
IUPAC Name(2E,4E,6Z,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid
Traditional Namealitretinoin
CAS Registry NumberNot Available
SMILES
C\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C\C(O)=O
InChI Identifier
InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8-,16-14+
InChI KeyInChIKey=SHGAZHPCJJPHSC-ZVCIMWCZSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassRetinoids
Direct ParentRetinoids
Alternative Parents
Substituents
  • Retinoid skeleton
  • Diterpenoid
  • Carbocyclic fatty acid
  • Medium-chain fatty acid
  • Methyl-branched fatty acid
  • Branched fatty acid
  • Fatty acyl
  • Fatty acid
  • Unsaturated fatty acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
  • Food
Biofunction
  • Cell signaling
  • Fuel and energy storage
  • Fuel or energy source
  • Membrane integrity/stability
Application
  • Nutrients
  • Stabilizers
  • Surfactants and Emulsifiers
Cellular locations
  • Extracellular
  • Membrane
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.0048 mg/mLALOGPS
logP5.66ALOGPS
logP5.01ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity97.79 m3·mol-1ChemAxon
Polarizability35.95 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biofluid Locations
  • Blood
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Retinol MetabolismSMP00074map00830
Vitamin A DeficiencySMP00336Not Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0042 +/-0.001 uMAdult (>18 years old)MaleNormal details
BloodDetected and Quantified0.0056 +/- 0.002 uMAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022982
KNApSAcK IDNot Available
Chemspider ID395778
KEGG Compound IDC15493
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkAvita
NuGOwiki LinkHMDB02369
Metagene LinkHMDB02369
METLIN IDNot Available
PubChem Compound449171
PDB IDNot Available
ChEBI ID50648
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Mertz JR, Shang E, Piantedosi R, Wei S, Wolgemuth DJ, Blaner WS: Identification and characterization of a stereospecific human enzyme that catalyzes 9-cis-retinol oxidation. A possible role in 9-cis-retinoic acid formation. J Biol Chem. 1997 May 2;272(18):11744-9. [9115228 ]

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Binds free retinal and cellular retinol-binding protein-bound retinal. Can convert/oxidize retinaldehyde to retinoic acid (By similarity).
Gene Name:
ALDH1A1
Uniprot ID:
P00352
Molecular weight:
54861.44
Reactions
9-cis-Retinal + NAD + Water → 9-cis-Retinoic acid + NADH + Hydrogen Iondetails
General function:
Involved in oxidoreductase activity
Specific function:
Recognizes as substrates free retinal and cellular retinol-binding protein-bound retinal. Does metabolize octanal and decanal but does not metabolize citral, benzaldehyde, acetaldehyde and propanal efficiently (By similarity).
Gene Name:
ALDH1A2
Uniprot ID:
O94788
Molecular weight:
54672.24
Reactions
9-cis-Retinal + NAD + Water → 9-cis-Retinoic acid + NADH + Hydrogen Iondetails
General function:
Involved in sequence-specific DNA binding transcription factor activity
Specific function:
Nuclear hormone receptor. Involved in the retinoic acid response pathway. Binds 9-cis retinoic acid (9C-RA)
Gene Name:
RXRB
Uniprot ID:
P28702
Molecular weight:
56921.4
General function:
Involved in sequence-specific DNA binding transcription factor activity
Specific function:
Nuclear hormone receptor. Involved in the retinoic acid response pathway. Binds 9-cis retinoic acid (9C-RA)
Gene Name:
RXRG
Uniprot ID:
P48443
Molecular weight:
50870.7
General function:
Involved in sequence-specific DNA binding transcription factor activity
Specific function:
Nuclear hormone receptor. Involved in the retinoic acid response pathway. Binds 9-cis retinoic acid (9C-RA). ARF6 acts as a key regulator of the tissue-specific adipocyte P2 (aP2) enhancer
Gene Name:
RXRA
Uniprot ID:
P19793
Molecular weight:
50810.8